How to convert the PDB file to PSF format?

VMD allows converting PDB to PSF format but sometimes it gives multiple errors. Therefore, in this article, we are going to convert PDB into PSF format using a different method.

We will use the ParmEd [1] package for that. You can download and install this package from here.

Let’s say we have a PDB file named, prot.pdb that we are trying to convert into PSF format.

#!/usr/bin/env python3

import parmed as pmd

structure = pmd.load_file('prot.pdb')

structure.save('prot.psf')

Save this file in Python format and run it. This will output ‘prot.psf’ file that you can also use in VMD.

1. Shirts, M.R., Klein, C., Swails, J.M. et al. (2017). Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des 31, 147–161.